reference b longum subsp infantis atcc 15697 genome (ATCC)

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ATCC reference b longum subsp infantis atcc 15697 genome
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Reference B Longum Subsp Infantis Atcc 15697 Genome, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1003 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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reference b longum subsp infantis atcc 15697 genome - by Bioz Stars, 2026-10

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1) Product Images from "Inefficient Metabolism of the Human Milk Oligosaccharides Lacto- N -tetraose and Lacto- N -neotetraose Shifts Bifidobacterium longum subsp. infantis Physiology"

Article Title: Inefficient Metabolism of the Human Milk Oligosaccharides Lacto- N -tetraose and Lacto- N -neotetraose Shifts Bifidobacterium longum subsp. infantis Physiology

Journal: Frontiers in Nutrition

doi: 10.3389/fnut.2018.00046

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Figure Legend Snippet: List of strains used in this study ^a .

Techniques Used:

B. longum subsp. infantis ATCC 15697 growth kinetics while utilizing milk carbohydrates. The final asymptotic OD 600 nm (A) and growth rate (k, h −1 ) (B) of B. infantis ATCC15697 subsisting on mMRS medium containing 2% (wt/v) galactose (Gal), lactose (Lac), lacto- N -tetraose (LNT), or lacto- N -neotetraose (LNnT). The growth kinetics was calculated with Wolfram Mathematica 10.3. The data depicts mean ± SD of three independent experiments. The single asterisk (*) indicates the significant differences between carbohydrate utilizations evaluated by one-way ANOVA and Tukey's multiple comparison ( p < 0.05).

Figure Legend Snippet: B. longum subsp. infantis ATCC 15697 growth kinetics while utilizing milk carbohydrates. The final asymptotic OD 600 nm (A) and growth rate (k, h −1 ) (B) of B. infantis ATCC15697 subsisting on mMRS medium containing 2% (wt/v) galactose (Gal), lactose (Lac), lacto- N -tetraose (LNT), or lacto- N -neotetraose (LNnT). The growth kinetics was calculated with Wolfram Mathematica 10.3. The data depicts mean ± SD of three independent experiments. The single asterisk (*) indicates the significant differences between carbohydrate utilizations evaluated by one-way ANOVA and Tukey's multiple comparison ( p < 0.05).

Techniques Used: Comparison

B. longum subsp. infantis ATCC 15697 fermentative endproducts while utilizing milk carbohydrates through the F6PPK pathway. Absolute concentrations of lactic acid (A) , acetic acid (B) , formic acid (C) , and ethanol (D) . In addition, acetic acid to lactic acid ratio (E) , formic acid to lactic acid ratio (F) , formic acid to acetic acid ratio (G) , and ethanol to lactic acid ratio (H) . All panels represent B. infantis ATCC15697 growing on mMRS medium containing 2% (wt/v) galactose (Gal), lactose (Lac), lacto- N -tetraose (LNT), or lacto- N -neotetraose (LNnT). Averages from independent biological replicates (triplicate or more) are shown with bars representing standard deviations of the means. The values for organic acid production are expressed in millimolar (mM) absolute concentration. A single asterisk (*) denotes significant differences between metabolite production evaluated by one-way ANOVA and Tukey's multiple comparison test ( p < 0.05).

Figure Legend Snippet: B. longum subsp. infantis ATCC 15697 fermentative endproducts while utilizing milk carbohydrates through the F6PPK pathway. Absolute concentrations of lactic acid (A) , acetic acid (B) , formic acid (C) , and ethanol (D) . In addition, acetic acid to lactic acid ratio (E) , formic acid to lactic acid ratio (F) , formic acid to acetic acid ratio (G) , and ethanol to lactic acid ratio (H) . All panels represent B. infantis ATCC15697 growing on mMRS medium containing 2% (wt/v) galactose (Gal), lactose (Lac), lacto- N -tetraose (LNT), or lacto- N -neotetraose (LNnT). Averages from independent biological replicates (triplicate or more) are shown with bars representing standard deviations of the means. The values for organic acid production are expressed in millimolar (mM) absolute concentration. A single asterisk (*) denotes significant differences between metabolite production evaluated by one-way ANOVA and Tukey's multiple comparison test ( p < 0.05).

Techniques Used: Concentration Assay, Comparison

Bifidobacterium longum subsp. infantis metabolic pathways for utilization of lacto- N -tetraose (LNT) and lacto- N -neotetraose (LNnT) and their constituent monosaccharides. LNT and LNnT translocate through the cell membrane facilitated by ABC transporters. Intracellular glycosyl hydrolases process HMO into constituent monosaccharides to enter the central fermentative pathway. This pathway involves the characteristic fructose-6-phosphate phosphoketolase (F6PPK) activity denoted in blue. Genes encoding intracellular metabolic enzymes are depicted next to arrows according to their locus tag in the ATCC 15697 genome. Solid arrows are direct conversions with dashed arrows depicting the sequential actions of multiple enzymes. Predicted catabolic operations that feed into the F6PPK pathway and their corresponding products are denoted as purple. Stoichiometric coefficients of secreted metabolites, ATP, and NAD + produced during metabolism are labeled in red. Experimental observations depicted in Figures , including stoichiometry are incorporated.

Figure Legend Snippet: Bifidobacterium longum subsp. infantis metabolic pathways for utilization of lacto- N -tetraose (LNT) and lacto- N -neotetraose (LNnT) and their constituent monosaccharides. LNT and LNnT translocate through the cell membrane facilitated by ABC transporters. Intracellular glycosyl hydrolases process HMO into constituent monosaccharides to enter the central fermentative pathway. This pathway involves the characteristic fructose-6-phosphate phosphoketolase (F6PPK) activity denoted in blue. Genes encoding intracellular metabolic enzymes are depicted next to arrows according to their locus tag in the ATCC 15697 genome. Solid arrows are direct conversions with dashed arrows depicting the sequential actions of multiple enzymes. Predicted catabolic operations that feed into the F6PPK pathway and their corresponding products are denoted as purple. Stoichiometric coefficients of secreted metabolites, ATP, and NAD + produced during metabolism are labeled in red. Experimental observations depicted in Figures , including stoichiometry are incorporated.

Techniques Used: Membrane, Activity Assay, Produced, Labeling

Growth kinetics of B. longum subsp. infantis strains subsisting on milk carbohydrates. The final asymptotic OD 600 nm and growth rate (k, h −1 ) of B. infantis strains while growing on mMRS medium containing 2% (wt/v) galactose (A) , lactose (B) , lacto- N -tetraose (LNT) (C) , and lacto- N -neotetraose (LNnT) (D) . The growth kinetics was calculated with Wolfram Mathematica 10.3 and represents the mean ± SD of three independent experiments. Purple and red bars indicate bacterial growth and growth rate respectively. The asterisks indicate the significant differences between strains evaluated by one-way ANOVA and Tukey's multiple comparison. * p < 0.05, ** p < 0.005, *** p < 0.0005, and **** p < 0.0001. The growth kinetics for glucose and GlcNAc were not included as not all strains consume these monosaccharides.

Figure Legend Snippet: Growth kinetics of B. longum subsp. infantis strains subsisting on milk carbohydrates. The final asymptotic OD 600 nm and growth rate (k, h −1 ) of B. infantis strains while growing on mMRS medium containing 2% (wt/v) galactose (A) , lactose (B) , lacto- N -tetraose (LNT) (C) , and lacto- N -neotetraose (LNnT) (D) . The growth kinetics was calculated with Wolfram Mathematica 10.3 and represents the mean ± SD of three independent experiments. Purple and red bars indicate bacterial growth and growth rate respectively. The asterisks indicate the significant differences between strains evaluated by one-way ANOVA and Tukey's multiple comparison. * p < 0.05, ** p < 0.005, *** p < 0.0005, and **** p < 0.0001. The growth kinetics for glucose and GlcNAc were not included as not all strains consume these monosaccharides.

Techniques Used: Comparison

Analysis of B. longum subsp infantis strains secreted fermentative endproducts while utilizing milk carbohydrates. Panel (A) shows metabolites secreted by B. infantis strains for each carbohydrate clustered by Euclidean distance calculated with MetaboAnalyst 3.0. The scaling was performed by mean-centering and dividing by the standard deviation of each metabolite. The red denotes lower concentrations of the metabolite with yellow approaching higher concentrations. Panels (B,E) display the 2D-principal component analysis (PCA) plot depicting acetic acid to lactic acid ratios and acetic acid to lactic acid to formic acid ratios respectively. The arrows in PCA plot represent the correlation of the variables with the principal components (PC1 and PC2). Points represent the scores of each component grouped as biological replicates. The ellipses for each strain incorporate 68% of the normal probability of the scores for corresponding strains. Panels (C,F) are hierarchical clustering dendrogram of strains according to acetic acid to lactic acid ratios and acetic acid to lactic acid to formic acid ratios using the Ward method and Euclidean distance. The y-axis measures the closeness of either individual strains or their calculated clusters. Panels (D,G) represent hierarchical clustering based on p -values calculated with multiscale bootstrapping between acetic acid to lactic acid ratio and acetic acid to lactic acid to formic acid ratio. The y-axis measures the closeness of either individual substrates or clusters according to two metrics: Approximately Unbiased p -value (AU in red) and Bootstrap Probability value (BP in blue). Clusters exhibiting AU values >95% are highlighted by rectangles.

Figure Legend Snippet: Analysis of B. longum subsp infantis strains secreted fermentative endproducts while utilizing milk carbohydrates. Panel (A) shows metabolites secreted by B. infantis strains for each carbohydrate clustered by Euclidean distance calculated with MetaboAnalyst 3.0. The scaling was performed by mean-centering and dividing by the standard deviation of each metabolite. The red denotes lower concentrations of the metabolite with yellow approaching higher concentrations. Panels (B,E) display the 2D-principal component analysis (PCA) plot depicting acetic acid to lactic acid ratios and acetic acid to lactic acid to formic acid ratios respectively. The arrows in PCA plot represent the correlation of the variables with the principal components (PC1 and PC2). Points represent the scores of each component grouped as biological replicates. The ellipses for each strain incorporate 68% of the normal probability of the scores for corresponding strains. Panels (C,F) are hierarchical clustering dendrogram of strains according to acetic acid to lactic acid ratios and acetic acid to lactic acid to formic acid ratios using the Ward method and Euclidean distance. The y-axis measures the closeness of either individual strains or their calculated clusters. Panels (D,G) represent hierarchical clustering based on p -values calculated with multiscale bootstrapping between acetic acid to lactic acid ratio and acetic acid to lactic acid to formic acid ratio. The y-axis measures the closeness of either individual substrates or clusters according to two metrics: Approximately Unbiased p -value (AU in red) and Bootstrap Probability value (BP in blue). Clusters exhibiting AU values >95% are highlighted by rectangles.

Techniques Used: Standard Deviation

Endproduct ratios of B. longum subsp. infantis strain fermentative endproducts while utilizing the milk carbohydrates. Acetic acid to lactic acid ratio (A) , acetic acid to lactic acid to formic acid ratio (B) , and ethanol to lactic acid ratio (C) . Colors indicate the following carbohydrate substrates: Purple, galactose; red, lactose; dark blue, lacto- N -tetraose; green, lacto- N -neotetraose. Averages from independent biological replicates (at least triplicate) are shown with bars representing standard deviation from the mean. The asterisks indicate the significant differences evaluated by two-way ANOVA and Tukey's multiple comparison. * p < 0.05, ** p < 0.005, *** p < 0.0005, and **** p < 0.0001.

Figure Legend Snippet: Endproduct ratios of B. longum subsp. infantis strain fermentative endproducts while utilizing the milk carbohydrates. Acetic acid to lactic acid ratio (A) , acetic acid to lactic acid to formic acid ratio (B) , and ethanol to lactic acid ratio (C) . Colors indicate the following carbohydrate substrates: Purple, galactose; red, lactose; dark blue, lacto- N -tetraose; green, lacto- N -neotetraose. Averages from independent biological replicates (at least triplicate) are shown with bars representing standard deviation from the mean. The asterisks indicate the significant differences evaluated by two-way ANOVA and Tukey's multiple comparison. * p < 0.05, ** p < 0.005, *** p < 0.0005, and **** p < 0.0001.

Techniques Used: Standard Deviation, Comparison

Gene expression of inflammatory marker Interleukin-8 in Caco-2 epithelial cells exposed to spent media following milk oligosaccharide fermentation. The y-axis represents the fold change in IL-8 expression relative to phosphate buffer solution (PBS). The x-axis depicts the sources of B. infantis metabolites which are used to treat Caco-2 cells after lipopolysaccharides (LPS) induction. The error bars show standard deviations of biological duplicates, each measured with three technical replicates. The single asterisks (*) indicate the significant differences evaluated by one-way ANOVA and Tukey's multiple comparison ( p < 0.05).

Figure Legend Snippet: Gene expression of inflammatory marker Interleukin-8 in Caco-2 epithelial cells exposed to spent media following milk oligosaccharide fermentation. The y-axis represents the fold change in IL-8 expression relative to phosphate buffer solution (PBS). The x-axis depicts the sources of B. infantis metabolites which are used to treat Caco-2 cells after lipopolysaccharides (LPS) induction. The error bars show standard deviations of biological duplicates, each measured with three technical replicates. The single asterisks (*) indicate the significant differences evaluated by one-way ANOVA and Tukey's multiple comparison ( p < 0.05).

Techniques Used: Gene Expression, Marker, Expressing, Comparison

other:

Article Title: Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome
Article Snippet: We aligned the infant gut metagenomic shotgun reads to the B. infantis ATCC 15697 reference genome, downloaded from NCBI, using bowtie2 v2.2.491.

Sequencing:

Article Title: Riboflavin Biosynthesis and Overproduction by a Derivative of the Human Gut Commensal Bifidobacterium longum subsp. infantis ATCC 15697.
Article Snippet: A whole transcriptome library was constructed using the TruSeq Stranded RNA LT Kit (Illumina, Inc.) and samples were loaded into a NextSeq High Output v2 Kit Chemicals 150 cycles (Illumina), according to the technical support guidelines. .. Following sequencing, the reads were depleted of adapters, quality filtered (with overall quality, quality window and length filters) and aligned to the B. infantis ATCC 15697 reference genome (genomic features model GTF file5) through bowtie2 aligner6. ..

Article Title: Riboflavin Biosynthesis and Overproduction by a Derivative of the Human Gut Commensal Bifidobacterium longum subsp. infantis ATCC 15697
Article Snippet: A whole transcriptome library was constructed using the TruSeq Stranded RNA LT Kit (Illumina, Inc.) and samples were loaded into a NextSeq High Output v2 Kit Chemicals 150 cycles (Illumina), according to the technical support guidelines. .. Following sequencing, the reads were depleted of adapters, quality filtered (with overall quality, quality window and length filters) and aligned to the B. infantis ATCC 15697 reference genome (genomic features model GTF file ) through bowtie2 aligner . ..

Generated:

Article Title: Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome.
Article Snippet: .. To generate network interaction plots between milk-expressed genes and infant fecal microbes identified in the sparse CCA analysis, for each significantly enriched pathway (q value < 10%) in a component, we (1) filtered for overlapping genes between the component and pathway; (2) generated a pairwise correlation matrix of mother-infant pairs’ trait values for those genes, the top 3 microbiome traits in the component with positive weights, and top 3 microbiome traits with negative weights; (3) pruned for correlations with Pearson’s r > 0.3 and p < 0.05; (4) generated a network plot from the pairwise correlation matrix using the ‘ggnetwork’ package in R.103 Cell Genomics 4, 100638, October 9, 2024 e8 B. infantis growth rates were estimated using Compute PTR (CoPTR).61 We aligned the infant gut metagenomic shotgun reads to the B. infantis ATCC 15697 reference genome, downloaded from NCBI, using bowtie2 v2.2.4.100 We then used CoPTR to get coverage information for each mapped sample, filtering for samples with at least 75% coverage and at least 3000 mapped reads to the B. infantis genome. ..

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